November 19, 2010

Besides haplogroups Q1a3a* (55; 85%), R (4; 6%) and E (2; 3%), the haplogroup C3* was determined in 4 out of 65 Waorani and Kichwa males (6%). In comparison to North American haplogroups, where C3b (defined by P39) is the most frequent in Native Americans, haplogroup C3* is more ancient. This finding is surprising, because in view of the hypothesis of the peopling of South America by Asians migrating by land through North America it was expected to find the same C lineage or a more derived one as in North America. With now six Y chromosomes belonging to the Central and Eastern Asian haplogroup C3* found in three tribes living in the Northwest of South America (Wayuu, Lowland Kichwa and Waorani) existing models of the entry and early distribution of settler in South America could be challenged.

Studying the Y chromosomes of indigenous tribes of Ecuador revealed a lack of strategic SNP assays to examine the substructure of South American native populations. In most studies dealing with South American samples so far only the most common Y-SNP M3 of haplogroup Q was analyzed, because this is known to define a founder group in South America. Studies of SNPs ancestral to Q-M3 (Q1a3a) to confirm the results or the typing of Q subclades have often been neglected. For this reason we developed a SNaPshot assay, which allows first for a hierarchical testing of all main haplogroups occurring in South American populations and second for a detailed analysis of haplogroups Q and C thought having ancient Asian descent. We selected 16 SNPs from the YCC haplogroup tree and established two multiplexes. The first multiplex ("SA Major") includes 12 Y-SNPs defining the most frequent haplogroups occurring in South America (M42, M207, M242, M168, M3, M145, M174, M213, RPS4Y711, M45, P170, and M9). The second multiplex ("SA SpecQ") contains Y-SNPs of haplogroup Q, especially of the subclade Q-M3 (M19, M194, P292, M3, and M199). Within our Ecuadorian sample, haplogroup Q-M3 (xM19, M194, P292, and M199) was predominant, but we also found haplogroup E and R, which can be attributed to recent admixture. Moreover, we found four out of 65 samples, which were tested to be haplogroup C3* (C-M217) the modal haplogroup in Mongolians and widespread in indigenous populations of the Russian Far East as well as in Eastern Asia. This haplogroup is not known to be the result of recent admixture and has been found only one time before in South America. Since haplogroup C occurs in Asia and in North America (C3b or C-P39), we assume that these C-lineages are ancient as well. Therefore, we established a third multiplex ("SA SpecC"), which allows the further subtyping of haplogroup C, mainly of subclade C3 defined by the Y-SNP M217 (M407, M48, P53.1, M217, P62, RPS4Y711, M93, M86, and P39). Altogether, these three multiplexes cover the most frequent haplogroups in South America and allow for a maximal resolution of the Y-chromosomal SNP diversity in Amerindian population samples.